forgi for plotting 2D RNA structure

Question

[galchenkova.mari]

Hi, everyone!

I need some help with forgi library for visualisation of RNA secondary structure.

I'd like from dot-bracket notation with known RNA sequence to plot 2D graph like that you can find here - https://viennarna.github.io/forgi/graph_tutorial.html.

If there any other possibilities to plot it in real-time (for instance, in jupyter notebook avoiding any crossing external scripts), I will be very thankful to learn them!

Thank you in advance

[Pierre Lindenbaum]

Hello galchenkova.mari!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/5642

This is typically not recommended as it runs the risk of annoying people in both communities.

[galchenkova.mari]

oh thanks!

I don't know that

Answer 1

[Pierre Lindenbaum]

(no tested)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459502/

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

Answer 2

[Wayne]

The OP mentioned Jupyter notebooks. There's a solution that works in Jupyter that's based on RNArtist as highlighted in a twitter post:

"Ready to play with the RNArtistCore language without installing anything? Give a try to the #jupyter notebook hosted on @mybinderteam. Click on the launch button from https://github.com/fjossinet/RNArtistCore-binder. Thanx to @Fomightez for the first version of this notebook"

In fact, the developer of it, Fabrice Jossinet, regular posts about the features and development here, and so the images there will give you a good feel for its abilities.
For example, as described here, RNArtist can easily get and plot RNA secondary structures from RNAcentral entries.

More at:

• RNArtist Gihub repo
• Launchable via MyBinder version of RNArtistCore
• RNArtist twitter feed highlighting development and features
• RNArtist Gallery